Variant chr12-57802018-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006576.4(AVIL):c.2151+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 956,428 control chromosomes in the GnomAD database, including 65,300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 7845 hom., cov: 32)

Exomes 𝑓: 0.37 ( 57455 hom. )

Consequence

AVIL
NM_006576.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.05

Variant links:

Genes affected

AVIL (HGNC:14188): (advillin) The protein encoded by this gene is a member of the gelsolin/villin family of actin regulatory proteins. This protein has structural similarity to villin. It binds actin and may play a role in the development of neuronal cells that form ganglia. [provided by RefSeq, Jul 2008]

AVIL links:

TSFM (HGNC:12367): (Ts translation elongation factor, mitochondrial) This gene encodes a mitochondrial translation elongation factor. The encoded protein is an enzyme that catalyzes the exchange of guanine nucleotides on the translation elongation factor Tu during the elongation step of mitchondrial protein translation. Mutations in this gene are associated with combined oxidative phosphorylation deficiency-3 syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2010]

TSFM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 12-57802018-T-C is Benign according to our data. Variant chr12-57802018-T-C is described in ClinVar as [Benign]. Clinvar id is 1226718.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AVIL	NM_006576.4 linkuse as main transcript	c.2151+142A>G		intron_variant		ENST00000549994.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AVIL	ENST00000549994.2 linkuse as main transcript	c.2151+142A>G		intron_variant		4	NM_006576.4	P1	O75366-1

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

43995

AN:

151922

Hom.:

7853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0878

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.403

Gnomad OTH

AF:

0.368

GnomAD4 exome

AF:

0.366

AC:

294743

AN:

804388

Hom.:

57455

AF XY:

0.363

AC XY:

146350

AN XY:

403574

show subpopulations

Gnomad4 AFR exome

AF:

0.0834

Gnomad4 AMR exome

AF:

0.267

Gnomad4 ASJ exome

AF:

0.454

Gnomad4 EAS exome

AF:

0.157

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.334

Gnomad4 NFE exome

AF:

0.401

Gnomad4 OTH exome

AF:

0.363

GnomAD4 genome

AF:

0.289

AC:

43967

AN:

152040

Hom.:

7845

Cov.:

AF XY:

0.286

AC XY:

21254

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.0875

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.226

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.403

Gnomad4 OTH

AF:

0.365

Alfa

AF:

0.244

Hom.:

872

Bravo

AF:

0.279

Asia WGS

AF:

0.198

AC:

689

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

DANN

Benign

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over